Variant report

Variant	rs942641
Chromosome Location	chr6:33687007-33687008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33684071..33687779-chr6:33863332..33865982,3	MCF-7	breast:
2	chr6:33670443..33672859-chr6:33684999..33687830,2	K562	blood:
3	chr6:33680227..33683145-chr6:33684696..33687420,2	K562	blood:
4	chr6:33674250..33675922-chr6:33684521..33687700,3	K562	blood:
5	chr6:33677229..33679959-chr6:33686466..33689322,3	K562	blood:
6	chr6:33676188..33679535-chr6:33684532..33687209,3	MCF-7	breast:
7	chr6:33684753..33687394-chr6:33728535..33731247,2	MCF-7	breast:
8	chr6:33680227..33683293-chr6:33684221..33688907,5	K562	blood:
9	chr6:33686485..33689308-chr6:34514444..34516167,2	MCF-7	breast:
10	chr6:33686168..33688632-chr6:33755438..33757308,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000249346	Chromatin interaction
ENSG00000137288	Chromatin interaction
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1014933	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947430	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10947434	0.90[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947435	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs11759396	0.90[JPT][hapmap]
rs1555965	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2147656	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2147657	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2229642	0.82[JPT][hapmap]
rs2274458	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2281829	0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2296739	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2296742	0.81[JPT][hapmap]
rs2966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3227	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3818521	0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3818523	0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs3818524	0.82[EUR][1000 genomes]
rs3818525	0.81[EUR][1000 genomes]
rs3818527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818529	0.81[EUR][1000 genomes]
rs3818530	0.89[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs4711336	0.81[JPT][hapmap]
rs4711338	0.81[JPT][hapmap]
rs4711339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711340	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4711343	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4713659	0.89[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs4713660	0.82[EUR][1000 genomes]
rs4713661	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713665	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713666	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713670	0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs4713671	0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs4713672	0.91[JPT][hapmap]
rs4713674	0.90[JPT][hapmap]
rs4713675	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs542441	0.81[JPT][hapmap]
rs560111	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs622917	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs626156	0.81[JPT][hapmap]
rs6457739	0.89[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6904816	0.90[CHB][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6916949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6917140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6919321	0.90[JPT][hapmap]
rs6928010	0.90[CHB][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6938056	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs749847	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs753890	0.81[EUR][1000 genomes]
rs754404	0.81[EUR][1000 genomes]
rs7739505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7759668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7770465	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs791902	0.91[JPT][hapmap]
rs791903	0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs9348924	0.89[JPT][hapmap]
rs9366828	0.85[EUR][1000 genomes]
rs9368773	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9368776	0.83[EUR][1000 genomes]
rs9380375	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9394163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs942640	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs942643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9469566	0.89[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs9469583	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs942641	ITPR3	cis	Whole Blood	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33680000-33689400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:33680000-33690000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:33680000-33690200	Weak transcription	Psoas Muscle	Psoas
4	chr6:33680000-33693000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:33680000-33695200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:33680000-33695800	Weak transcription	Spleen	Spleen
7	chr6:33680000-33696200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:33680000-33698400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:33680000-33705000	Weak transcription	Brain Angular Gyrus	brain
10	chr6:33681800-33689200	Enhancers	Pancreas	Pancrea
11	chr6:33684200-33687400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:33684200-33688200	Enhancers	Fetal Lung	lung
13	chr6:33684400-33688000	Weak transcription	Gastric	stomach
14	chr6:33684600-33688200	Enhancers	Fetal Brain Male	brain
15	chr6:33684600-33688600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:33685000-33687400	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr6:33685200-33688000	Weak transcription	GM12878-XiMat	blood
18	chr6:33685200-33693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:33686000-33688000	Enhancers	Brain Substantia Nigra	brain
20	chr6:33686200-33687400	Enhancers	Esophagus	oesophagus
21	chr6:33686200-33700200	Weak transcription	Liver	Liver
22	chr6:33686400-33689600	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:33686400-33689600	Weak transcription	Placenta	Placenta
24	chr6:33686400-33691600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:33686400-33691800	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:33686600-33687200	Weak transcription	Brain Anterior Caudate	brain
28	chr6:33686600-33687400	Flanking Active TSS	Stomach Mucosa	stomach
29	chr6:33686600-33687400	Enhancers	NHEK	skin
30	chr6:33686600-33688600	Weak transcription	Left Ventricle	heart
31	chr6:33686600-33688800	Weak transcription	HSMM	muscle
32	chr6:33686600-33689600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr6:33686600-33689600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:33686600-33689800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:33686600-33690000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:33686600-33690600	Weak transcription	Right Ventricle	heart
37	chr6:33686600-33695800	Weak transcription	Right Atrium	heart
38	chr6:33686600-33698600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:33686800-33688000	Weak transcription	Lung	lung
40	chr6:33686800-33689200	Weak transcription	HSMMtube	muscle
41	chr6:33687000-33688600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:33687000-33688600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:33687000-33688800	Weak transcription	HMEC	breast

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